1Q3F

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.

Bianchet, M.A.Seiple, L.A.Jiang, Y.L.Ichikawa, Y.Amzel, L.M.Stivers, J.T.

(2003) Biochemistry 42: 12455-12460

  • DOI: 10.1021/bi035372+
  • Primary Citation of Related Structures:  
    1Q3F

  • PubMed Abstract: 
  • The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbeniu ...

    The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.


    Organizational Affiliation

    Departments of Biophysics, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil-DNA glycosylase A223Homo sapiensMutation(s): 0 
Gene Names: UNG OR DGU OR UNG15UNGDGUUNG1UNG15
EC: 3.2.2 (PDB Primary Data), 3.2.2.27 (UniProt)
Find proteins for P13051 (Homo sapiens)
Explore P13051 
Go to UniProtKB:  P13051
NIH Common Fund Data Resources
PHAROS:  P13051
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3'B9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3'C10N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      URA
      Query on URA

      Download Ideal Coordinates CCD File 
      B
      URACIL
      C4 H4 N2 O2
      ISAKRJDGNUQOIC-UHFFFAOYSA-N
       Ligand Interaction
      PO4
      Query on PO4

      Download Ideal Coordinates CCD File 
      A
      PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.90 Å
      • R-Value Free: 0.235 
      • R-Value Work: 0.190 
      • R-Value Observed: 0.190 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 48.64α = 90
      b = 65.89β = 90
      c = 99.41γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      MOLREPphasing
      CNSrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-03-23
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2015-10-07
        Changes: Structure summary